BN0347 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.9024e-06 1.0244e-05
Layer 5 8.6635e-06 1.2169e-04
Layer 3 1.6202e-05 6.3361e-04
Layer 6 6.5132e-05 2.5176e-03
Layer 2 2.1148e-04 3.9581e-02
Layer 1 4.2128e-01 4.2204e-01
WM 9.9904e-01 7.0301e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.8770 0.8376
MORF4L2 Layer 4 2.8594 0.8357
SYP Layer 4 2.8340 0.8348
DCLK1 Layer 5 2.8516 0.8335
ATP6V1B2 Layer 5 2.8906 0.8334
SV2A Layer 4 2.8027 0.8316
BMERB1 Layer 4 2.9805 0.8289
PSMC5 Layer 4 2.7363 0.8260
CAPNS1 Layer 4 2.7129 0.8242
NDRG4 Layer 4 2.8711 0.8236
MYO5A Layer 4 2.8281 0.8212
REEP5 Layer 4 3.0391 0.8207
SEPTIN3 Layer 5 2.5215 0.8197
CAMK2G Layer 4 3.0781 0.8196
KLHDC3 Layer 4 2.8027 0.8191
MOAP1 Layer 4 2.8906 0.8167
NAPA Layer 4 2.9531 0.8166
DNAJC6 Layer 4 2.7129 0.8160
EIF1B Layer 4 3.0254 0.8155
CPLX1 Layer 5 2.8223 0.8152
PPP2CA Layer 5 2.6484 0.8146
CLTC Layer 4 2.6953 0.8145
TUBB Layer 4 2.8457 0.8141
RNF187 Layer 5 2.7598 0.8136
TAGLN3 Layer 4 2.8086 0.8134
B4GAT1 Layer 4 2.6309 0.8124
RTL8C Layer 4 2.6016 0.8116
FKBP8 Layer 5 2.6543 0.8114
VDAC1 Layer 4 2.7969 0.8112
TTC9B Layer 5 3.1055 0.8104
RAN Layer 4 2.6895 0.8101
NAP1L5 Layer 4 2.7852 0.8099
TUBA4A Layer 4 2.9863 0.8099
ATP6V1A Layer 5 2.7480 0.8095
COX5A Layer 4 2.7129 0.8090
SH3GL2 Layer 4 2.6074 0.8083
CEND1 Layer 4 2.9805 0.8083
SULT4A1 Layer 4 2.8965 0.8082
SLC24A2 Layer 5 2.8516 0.8078
PRKAR1A Layer 4 2.7852 0.8077
PINK1 Layer 4 2.7363 0.8071
EIF4H Layer 4 2.7422 0.8068
ANXA6 Layer 5 2.7188 0.8068
SPOCK1 Layer 4 2.7715 0.8061
DCTN2 Layer 4 2.8770 0.8060
SCOC Layer 5 2.6953 0.8058
NDUFV1 Layer 4 2.7422 0.8057
FAIM2 Layer 4 2.7852 0.8049
FHL1 Layer 4 3.2715 0.8048
INA Layer 4 2.7656 0.8047

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0347
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0347_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0347/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0347/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0347/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0347/report/PD/BN0347_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0347/report/PD/BN0347_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-10 22:45:19
  • Number of Processes: 10
  • Spending Time: 0h 4m